I don't see the article arguing that all maps should be replaced with this visualization. It's a much better map for certain tasks. Of course you lose information by throwing out geography.
I love the London tube map, but when I lived there, it was all the more useful to me because I look at other maps so that I could know that certain stations were in easy walking distance from each other or some other place I was going to.
Canonical answer: Queensway to Bayswater
Tube route: Queensway → Notting Hill Gate change train Notting Hill Gate → Bayswater The journey time between these two London underground stations is approximately 15 minutes
Or just walk. It takes 2 minutes.
I guess that when your abstraction is at the level of start station and end station, that is where the value of the tube map is.